The study of microbial phylogeny and evolution has emerged as an interdisciplinary synthesis, divergent in both methods and concepts from the classical evolutionary biology. The deployment of macromolecular sequencing in microbial classification has provided a deep evolutionary taxonomy hitherto deemed impossible. Microbial phylogenetics has greatly transformed the landscape of evolutionary biology, not only in revitalizing the field in the pursuit of life’s history over billions of years, but also in transcending the structure of thought that has shaped evolutionary theory since (...) the time of Darwin. A trio of primary phylogenetic lineages, along with the recognition of symbiosis and lateral gene transfer as fundamental processes of evolutionary innovation, are core principles of microbial evolutionary biology today. Their scope and significance remain contentious among evolutionists. (shrink)

The paper focuses on the semiotic principles of the organisation of ecosystems, attempting to find concepts that point to relations and not to elements. (1) Consortium (the term introduced by Johannes Reinke around 1873) can be defined as a group of organisms connected via (sign) relations, or groups of interspecific semiosic links in biocoenosis. The consortial relations include trophic and topic relations, both implying a recognition (identification) of the object by an organism involved (these, i.e., are sign relations). These relations (...) are ecologically inheritable. (2) Umwelt (the term introduced by Jakob von Uexküll around 1909) can be defined as a set of relations an organism has in an ecosystem (as in a semiosphere). The formation of an umwelt is dependent on the modelling system of the organism. (3) Biophony (the term introduced by Bernie Krause around 2000) denotes the coordination of inter- and intra-species relations in a soundscape of a biological community. This can be seen as a special case of Komposition as defined by Jakob and Thure von Uexküll. (4) Ecological code (as introduced, e.g. by Alexander Levich around 1977) can be defined as the set of (sign) relations (regular irreducible correspondences) characteristic to an entire ecosystem. We also mention the concepts of ecomones and coactones (introduced by Marcel Florkin in 1965) as the substances which are responsible for mediation of ecological inter-individual relations. All the relations as sign-relations evidently imply both a static or structuralist description (in terms of codes), and a processual description (in terms of semiosis carried on by interpretation). We conclude that all the above mentioned concepts can be viewed as conceptually connected and are suitable for semiotic description of biological communities. (shrink)